DNA-aptamer-nanographene oxide as a targeted bio-theragnostic system in antimicrobial photodynamic therapy against Porphyromonas gingivalis

The aim of this study was to design and evaluate the specificity of a targeted bio-theragnostic system based on DNA-aptamer-nanographene oxide (NGO) against Porphyromonas gingivalis during antimicrobial photodynamic therapy (aPDT). Following synthesis and confirmation of NGO, the binding of selected labeled DNA-aptamer to NGO was performed and its hemolytic activity, cytotoxic effect, and release times were evaluated. The specificity of DNA-aptamer-NGO to P. gingivalis was determined. The antimicrobial effect, anti-biofilm potency, and anti-metabolic activity of aPDT were then assessed after the determination of the bacteriostatic and bactericidal concentrations of DNA-aptamer-NGO against P. gingivalis. Eventually, the apoptotic effect and anti-virulence capacity of aPDT based on DNA-aptamer-NGO were investigated. The results showed that NGO with a flaky, scale-like, and layered structure in non-cytotoxic DNA-aptamer-NGO has a continuous release in the weak-acid environment within a period of 240 h. The binding specificity of DNA-aptamer-NGO to P. gingivalis was confirmed by flow cytometry. When irradiated, non-hemolytic DNA-aptamer-NGO were photoactivated, generated ROS, and led to a significant decrease in the cell viability of P. gingivalis (P < 0.05). Also, the data indicated that DNA-aptamer-NGO-mediated aPDT led to a remarkable reduction of biofilms and metabolic activity of P. gingivalis compared to the control group (P < 0.05). In addition, the number of apoptotic cells increased slightly (P > 0.05) and the expression level of genes involved in bacterial biofilm formation and response to oxidative stress changed significantly after exposure to aPDT. It is concluded that aPDT using DNA-aptamer-NGO as a targeted bio-theragnostic system is a promising approach to detect and eliminate P. gingivalis as one of the main bacteria involved in periodontitis in periopathogenic complex in real-time and in situ.

www.nature.com/scientificreports/ RNA) called "aptamers" are third-generation molecular probes that can tightly bind to their target molecule with high affinity 23,24 . Aptamers are selected in vitro from a synthesized random library using systematic evolution of ligands by exponential enrichment (SELEX) 25,26 . In cell-SELEX, the whole of the cell has been shown to be targeted. Aptamers can be considered cost-effective diagnostic methods that overcome the side effects of therapeutic agents and drug resistance of microbial pathogens. They can bind specifically to the surface factors of microorganisms, block the function of target proteins, and therefore be used as a basis for developing new therapies for infections 22 . Therefore, the use of aptamers in drug delivery systems has been considered due to their properties.
Accordingly, in the present study, the use of aptamer in addition to the specific identification of P. gingivalis as a photosensitizer carrier (NGO) is suggested. In this study, the synthesized NGO was first bonded to a DNAaptamer that has been selected against P. gingivals, and its physical stability, hemolytic effect, and cytotoxicity potential were evaluated. Next, the specificity of DNA-aptamer-NGO to P. gingivalis was monitored. After evaluation of endogenous ROS production, the antimicrobial, anti-biofilm, and anti-metabolic activities of aPDT based on DNA-aptamer-NGO against P. gingivalis were assessed. Finally, the apoptotic effects of aPDT using DNA-aptamer-NGO in human gingival fibroblast cells and the expression of genes involved in P. gingivalis pathogenesis were evaluated. The hypothesis in this study is that aptamer with specific binding to P. gingivalis firstly the other beneficial microorganisms are not affected by targeted aPDT, and secondly increases the antimicrobial and anti-biofilm effects of NGO-based aPDT without induction of apoptosis in normal human gingival fibroblast (HGF) cells.

Materials and methods
Synthesis of NGO. The synthesis of NGO oxide was performed using modified Hummer's method 27 in following manner: 3 g of graphite powder was added to a mixture of 69 mL sulfuric acid (H 2 SO 4 , 98%) and sodium nitrate (NaNO 3 , 1.5 g) in an ice bath for 2 h. 9 g of powdered potassium permanganate (KMnO4, 99%) was then slowly added to the mixture under continuous stirring at a temperature lower than 14 °C. The ice bath was removed after 2 h of stirring and the mixture was stirred until it turned dark green. 100 mL of distilled water was added slowly to the reaction mixture and the solution was then sonicated for 30 min. After that, 2 mL of 30% H 2 O 2 was added dropwise to the suspension causing the color to turn yellow, indicating the termination of the reaction. Finally, the mixture was centrifuged and rinsed with 10% HCl solution to remove the remaining metal ions. The GO powder was collected through filtration and dried under a vacuum.
Characterization of NGO. The surface morphology of the prepared NGO was evaluated with field emission scanning electron microscopy (FESEM, ZEISS, Germany). The particle size and zeta potential of nanoparticles were characterized by a MALVERN Zetasizer Ver. 6.01 (Malvern Instruments, UK). Fourier-transform infrared (FTIR) analysis was performed using a spectrum of two spectrophotometers (45° ZnSe crystal, Perki-nElmer Inc., US) in the range of 500-4000 cm −1 .
Binding of DNA-aptamer to NGO. Nucleotide sequences of aptamer specific to P. gingivalis were selected based on Park et al. study 28 . The sequence of the aptamer was optimized and modified by fluorescein amidites (FAM) based on the previous study 29 . The structure of the aptamer is shown in Fig. 2. The sequence of the FAMlabeled DNA-aptamer was 5'-TAT GCC AGC ATT TCG CCA ACG GTG GTC ATA CAG TGT GAA-3' . The binding of labeled DNA-aptamer to NGO was performed by the modified Lin et al. method 30 . Briefly, the oligonucleotide sequence was exposed to 40 μg/mL of NGO and allowed to react. After 2 h of reaction, 1% NaCl solution (1 M) was added and the solution was maintained at 4 °C for 30 min. The mixture was then incubated at 25, 45, 60, and 90 °C for 1 h. The resulting mixture was centrifuged at 16,000 rpm for 45 min and the residues were resuspended with phosphate-buffered saline (PBS; pH ~ 7.4). After three centrifugations and washing cycles, the aptamer-NGO was obtained. Afterward, the fluorescence intensities of the mixtures were recorded using a spectrophotometer. The emission spectra and the excitation wavelength were measured at 510 and 480 nm, respectively.
Evaluation of binding of DNA-aptamer-NGO composite to the P. gingivalis. To direct evidence of the binding of DNA-aptamer-NGO composite material to the P. gingivalis as the target, we compared the change in cell size after exposure of P. gingivalis cells to the DNA-aptamer-NGO composites with the control group (untreated P. gingivalis) using fluorescence intensity assay and FESEM. In brief, fresh supplemented BHI bacterial cultures, in the logarithmic growth phase (9-12 h old; adjusted to a concentration of 10 8 CFU/mL), were treated with the composites (250 nM) for10 min. Upon centrifugation at 6000 rpm for 8 min, the bacterial cells were collected and washed with PBS (pH 7.5) twice to remove unattached DNA-aptamer-NGO composite material and then resuspended in sterile distilled water. The bacterial suspension was filtered through a 0.2 μm polycarbonate filter to reassure the removal of unattached DNA-aptamer-NGO composite material and the filters containing bacterial cells as specimens were used for fluorescence intensity assay and FESEM. In the fluorescence intensity assay the restoration of fluorescent intensity to the samples was measured using a fluorescence spectrophotometer using excitation and emission wavelengths of 492 and 532 nm, respectively. In the FESEM, samples were fixed in a glutaraldehyde solution ( www.nature.com/scientificreports/ acid buffer, pH 7.5) as described in our previous study 31 . The specimens were rinsed with the sodium cacodylate/ hydrochloric acid buffer two times, followed by post fixing with 1% aqueous osmium tetroxide and dehydrated with graded ethanol solutions (50% for 30 min, 75%, 85%, and 95% each for 10 min, and 100% for 10 min). After critical point drying to remove ethanol completely, the specimens were mounted onto a stub, coated by gold sputter, and examined by FESEM as previously described 31 . To verify the detection of the P. gingivalis as the target bacterium, the fluorescent increment depending on an increment of cell numbers (10 2 , 10 4 , and 10 6 CFU/ mL) was assessed using DNA-aptamer-NGO composites (250 nM) based on the fluorescence intensity assay used in the evaluation of the binding of DNA-aptamer-NGO composite to the P. gingivalis. The intensities of FAM-DNA aptamer-NGOs (250 nM, 500 nM, and 1000 nM without any bacterial cells) also were measured according to the fluorescence intensity technique.
Evaluation of in vitro effect of pH on aptamer binding. The effects of pH value on aptamer binding were evaluated as described previously 32 . Briefly, following the preparation of the DNA-aptamer-NGO composite, it was washed using buffer A (1 Mm MgCl 2 , 150 mM NaCl, 25 mM HEPES, pH 7.6) and centrifugation of the mixture at 15,000 rpm for 20 min to remove unbound aptamers. The DNA-aptamer-NGO composite pellet was then dissolved in bacterial (P. gingivalis) suspension (10 6 CFU/mL). After that, the ionic strength of the suspension was adjusted to high using buffer A (150 mM NaCl, 25 mM HEPES, pH 7.6). Fluorescence intensities of the suspension were then measured following acidification and alkalization by incubating with citrate buffer (1 M; pH 5.5) and sodium bicarbonate (NaHCO 3 ; 1 M; pH 8.5), respectively using a UV-Vis spectrophotometer at 430 nm.
Hemolysis assays. The biocompatibility of DNA-aptamer-NGO composite based on ASTM standard E2524-08 (Standard Test Method for Analysis of Hemolytic Properties of Nanoparticles) 33 was determined using measurement of the hemolytic activity of the composite, as described by Isnansetyo and Kamei 34 . Briefly, a human whole blood sample obtained from returned unused blood bags in the blood bank (Iranian Blood Transfusion Organization) was centrifuged at 900 g for 2 min and then washed three times with phosphate-buffered saline (PBS; pH ~ 7.4) and diluted in PBS (330 μL of human whole blood per 10 ml of PBS). 0.2 mL of the diluted human whole blood sample was mixed with 0.8 mL of DNA-aptamer-NGO at the different concentrations (250, 500, and 1000 nM). The mixtures were incubated at a 37 °C water bath for 1 h. After the incubation, the samples were centrifuged at 800 g for 15 min and the absorbance of the supernatant was analyzed by a UV-Vis spectrophotometer at 540 nm. PBS (pH ~ 7.4) was chosen as a negative control since it is compatible with blood cells. Distilled water (pH ~ 7.4) was applied as a positive control due to its high hemolytic activity. Hemolysis assays were done in triplicate. The hemolytic activity results of DNA-aptamer-NGO in different concentrations as the samples expressed as percentage hemolysis with respect to negative and positive controls as follows: were seeded at a density of 1 × 10 5 cells/well in a 96-well microtiter plate containing Dulbecco's modified Eagle medium (Gibco, Grand Island, NY) supplemented with 10% fetal bovine serum (Gibco), 2% l-glutamine, 100 U/ mL penicillin, and 100 g/mL streptomycin (all purchased from Sigma-Aldrich, Germany). The microtiter plate was incubated at 37 °C in a humidified atmosphere of 5% CO 2 in the air for 24 h. After cells washing with PBS DNA-aptamer-NGO at the different concentrations (250, 500, and 1000 nM) were added to triplicate wells and kept for 24 h. After re-washing, the viability of HGF cells was assessed using MTT [3-(4,5-dimethylthiazol-2-yl)-2,5-diphenylte-trazolium bromide] kit according to the manufacturer's instructions. Finally, the optical density (OD) at 570 nm was measured by a microtiter plate.
Monitoring of specificity of DNA-aptamer-NGO to P. gingivalis. The specificity of binding of the FAM-labeled aptamer-NGO to P. gingivalis was assessed using flow cytometry. Briefly, 250 nM of FAM-labeled aptamer was incubated with 10 6 CFU/mL of P. gingivalis as the target cell and different bacteria such as Streptococcus mutans, Enterococcus faecalis, and Aggregatibacter actinomycetemcomitans as the non-target cells at 37 °C for 2 h. After washing with PBS three times, the bacteria cells were resuspended in PBS (300 μL). The fluorescence intensity of bacteria was measured by flow cytometry based on the previous study 35 .

Determination of bacteriostatic and bactericidal concentrations of DNA-aptamer-NGO against P. gingivalis.
To determine the minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) of DNA-aptamer-NGO as the bacteriostatic and bactericidal concentrations, respectively, we followed the procedure by acting according to our previous study 36 . In brief, after adding 100 µL of BHI broth supplemented with hemin and menadione to each well of a 96-well microtiter plate, 100 µL of 2000 nM DNA-aptamer-NGO was added to the well in column one and diluted twofold step-wise to column ten. Then, 100 µL/well of bacterial suspension with a concentration of 1.0 × 10 6 CFU/mL was transferred to each well. The microtiter plate was incubated under anaerobic conditions at 37 °C for 24 h. According to Clinical and Laboratory Standards Institute (CLSI) guidelines 37 , MIC was determined as the lowest concentration of DNAaptamer-NGO that completely inhibits visible bacterial growth, and MBC was determined by sub-culturing the test dilution on BHI agar plates that caused at least 99.999% killing of the initial inoculum.
Light source. In this study, a DenLase, Diode Laser Therapy System (Daheng Group Inc., China) equipped with 980 nm wavelength, a power of 1 W, a continuous-wave operation, and fiber of 400 μm was used as a light source 38 .
Evaluation of endogenous ROS production. In this study, endogenous ROS generation was quantified by fluorescence spectroscopy using 2′,7′-dichlorofluorescein diacetate (H 2 DCF-DA) according to the previous study 39 . Overnight culture of P. gingivalis was centrifuged (10,000 rpm for 15 min) and the pellets were washed and resuspended in PBS to achieve the cell density of 10 8 CFU/mL followed by incubation with 10 μM DCFH-DA. After 10 min of incubation, the bacterial cells were treated with 1/2 × and 1/4 × MIC of DNA-aptamer-NGO and exposed to the diode laser light for 1 min. In only light and only DNA-aptamer-NGO treated groups, the cells were exposed to the laser light without DNA-aptamer-NGO, and DNA-aptamer-NGO without laser light, respectively, while the control group (only bacterial cells) was left untreated. Thereafter, the fluorescence intensity produced from DCFH-DA was measured by a fluorescence spectrophotometer at an excitation wavelength of 488 nm and an emission wavelength of 535 nm.
Antimicrobial effect of aPDT based on DNA-aptamer-NGO against P. gingivalis in planktonic form. The antimicrobial effect of aPDT against P. gingivalis was determined as described by Pourhajibagher et al. 40 . Briefly, 100 µL of 1/2 × and 1/4 × MIC of DNA-aptamer-NGO was added to the wells after the addition of enriched BHI broth (100 µL) to each well of a 96-well microtiter plate. 100 µL/well of P. gingivalis suspension at the concentration of 1.0 × 10 6 CFU/mL was then added to each well. The suspension was incubated under dark, anaerobic conditions for 5 min and immediately exposed to the diode laser irradiation. Eventually, 10 µL of each well was spread onto the enriched BHI agar and the plates were incubated at 37 °C for 48 h in an anaerobic condition to determine P. gingivalis Log 10 CFU/mL.

Anti-biofilm effect of aPDT based on DNA-aptamer-NGO against P. gingivalis. P. gingivalis bio-
film was formed in a 96-well microtiter plate according to the previous study 41 . Briefly, 200 μL of P. gingivalis suspension at a final concentration of 1.5 × 10 8 CFUs/mL was added to each well of a 96-well microtiter plate and incubated at 37 °C for 48 h to allow biofilm formation. Prior to the treatment, the remaining non-adherent bacteria were removed by washing with PBS. After that, the preformed biofilm was incubated with 1/2 × and 1/4 × MBC of DNA-aptamer-NGO in the dark for 5 min and then treated with the diode laser. Biofilms in all the wells were subsequently stained using 100 μL of 0.1% crystal violet. After 15 min of incubation at room temperature, the wells were washed with PBS and the unbound dye was removed from the cells with 100 μL of 95% Estimation of the apoptotic effects of aPDT based on DNA-aptamer-NGO by flow cytometry. 1 × 10 6 cells/mL of HGF cells were cultured in a 96-well microtiter plate and incubated under the conditions mentioned above. 24 h later, DNA-aptamer-NGO at concentrations of 1/2 × and 1/4 × MIC were added to the culture medium. After six h, the cells in the DNA-aptamer-NGO-aPDT group were exposed to the diode laser light for 1 min. The cells were then washed with ice-cold PBS. The washed cells were re-suspended in 1 × binding buffer, and then 5 μL Annexin V-FITC was added followed by 5 μL propidium iodide (PI). The cells were incubated at room temperature in the dark for 15 min, and the percent of apoptotic cells was then determined by flow cytometry.

Quantification of the expression of genes via reverse transcription-quantitative real-time PCR (RT-qPCR).
Immediately after treatment of P. gingivalis by aPDT based on 1/2 × and 1/4 × MIC of DNAaptamer-NGO, the cells were pelleted and total RNA was extracted using the super RNA extraction Kit (AnaCell, Iran) in accordance with the manufacturer's instructions. The extracted RNAs were first treated with RNase-free DNase I treatment (Thermo Scientific GmbH, Germany) to eliminate the genomic DNAs, and cDNAs were then synthesized using random hexamer primed reactions using a Revert Aid First Strand cDNA Synthesis Kit (Thermo Fisher Scientific, US), according to the manufacturer's protocol. The gene-specific primers were designed according to our previous studies [43][44][45] and listed in Table 1. RT-qPCR was performed using Line-GeneK Real-Time PCR Detection System and Software (Bioer Technology, Hangzhou, China) under the cycling conditions included 95 °C for 5 min, followed by 40 cycles of 95 °C for 15 s, 60 °C for 10 s, and 72 °C for 10 s. The relative fold change was calculated using Livak and Schmittgen (2 −ΔΔCT ) method 46 .
Statistical analysis. All assays were set up in triplicate, and the results were expressed as mean values ± standard deviations (mean ± SD). Statistical significance was determined by two-way analysis of variance (ANOVA) and Tukeys' test in SPSS statistical software version 23. All experiments were performed in at least triplicate. P-values of less than 0.05 were considered to be statistically significant.
Ethics approval and consent to participate. The study was approved by the Ethics Committee of Tehran University of Medical Sciences (Application No. IR.TUMS.DENTISTRY.REC.1399.253), and all methods were carried out in accordance with relevant guidelines and regulations.

Results
Confirmation of NGO synthesis. The FESEM image of NGO in Fig. 3a exhibits transparent rippled silklike waves or a flaky, scale-like, layered structure, and wrinkled edge. Figure 3b shows the FTIR spectra of the NGO in the range of 500-4000 cm −1 , in which the peaks at 1402 cm −1 and 3432 cm −1 indicate the vibrational bands of O-H. C-O stretching, C=C stretching, and C=O stretching are observed at 1225 cm −1 , 1642 cm −1 , and 1736 cm −1 , respectively. The peak at 1068 cm −1 is attributed to a stretching vibration from the C-O-C bonds of epoxy or alkoxy groups. According to the results in Fig. 3c and d, the average size and the zeta potential of NGO were 21.3 ± 3.2 nm and −17.1 mV, respectively.  Confirmation of binding of DNA-aptamer to the NGO using atomic force microscopy (AFM). The binding of DNA-aptamer to the NGO and formation of DNA-aptamer-NGO composite was verified by AFM. As shown in Fig. 5a, the NGO sheet thickness is 0.34 nm. However, DNA-aptamer-NGO with a thickness of 1.00 nm showed that FAM-aptamer has been absorbed into the NGO surface successfully (Fig. 5b).

Confirmation of binding of DNA-aptamer-NGO composite material to the P. gingivalis. FESEM
investigation indicates that the untreated P. gingivalis cells have rod-like shape (length, 1.99 ± 0.36 μm; diameter, 1.23 ± 0.12 μm) and intact surfaces (Fig. 5c). After exposure to DNA-aptamer-NGO composite for ten min, the mean size of bacteria increased (length, 2.66 ± 0.37 μm; diameter, 1.52 ± 0.22 μm; Fig. 5d) without change in the shape of bacteria which shows evidence for binding of DNA-aptamer-NGO composite material to the P. gingivalis as the target.
The effect of pH on aptamer binding. The effect of different pH values on aptamer binding was shown in Fig. 6. Under the alkaline (pH 8.5) and acidic (pH 5.5) conditions, positive and adverse effects on aptamer Hemolysis assay. As shown in Fig. 7, high concentrations of DNA-aptamer-NGO incubated for 24 h with human red blood cells did not exceed 5%. The non-hemolytic character confirms the hemocompatibility of DNA-aptamer-NGO, which was similar to the PBS as a negative control.

Cytotoxicity effect of DNA-aptamer-NGO on human gingival fibroblast cell. The MTT assay was
performed to evaluate the gingival fibroblast cytotoxicity of DNA-aptamer-NGO. At different concentrations of DNA-aptamer-NGO, the mean percentage of HGF cells viability ranges from 95.2% to 87.6% (Fig. 8). Although the mean percentage of fibroblast viability decreases as the concentrations of DNA-aptamer-NGO (250, 500, and 1000 nM) increases, these reductions were not significant compared to the control group (untreated cells; P > 0.05).
Monitoring of specificity of DNA-aptamer-NGO to P. gingivalis. Fluorescently labeled DNAaptamer-NGO was analyzed against different species of bacteria, including A. actinomycetemcomitans, E. faecalis, P. gingivalis, and S. mutans. According to the results, the positive count (fluorescence intensity > 10) of P. gingivalis was significantly higher than that of the other bacteria (relative positive rate of 88.3%), indicating that the DNA-aptamer-NGO was of preferential binding affinity to P. gingivalis. As shown in Fig. 9, DNA-aptamer-NGO seemed to be of lower affinity to S. mutans (relative positive rate of 9.1%) among the other bacteria.   www.nature.com/scientificreports/ Re-culturing (subculturing) broth dilutions at and above the MIC (≤ 62.5 nM) onto BHI agar supplemented with hemin and menadione revealed that DNA-aptamer-NGO at concentrations ≥ 125 nM was prevented the growth of the P. gingivalis on the agar plate. So, the minimum bactericidal concentration (MBC) of DNAaptamer-NGO was 125 nM which implied nonviable P. gingivalis on the plate.

Determination of MIC and MBC
Evaluation of endogenous ROS production. aPDT groups using 1/2 × and 1/4 × MIC of DNAaptamer-NGO plus irradiation of diode laser demonstrated the enhanced ROS production by 1.95-and 1.51fold compared with the control group (untreated P. gingivalis), respectively (P < 0.05; Fig. 10), which was dosedependent. Also, the results revealed an increase (1.29-fold) in microbial suspension exposed to 1/2 × MIC of DNA-aptamer-NGO alone, while no significant increase in the DCFH-DA fluorescence was observed in P. gingivalis suspension subjected to diode laser alone and 1/4 × MIC of DNA-aptamer-NGO (P > 0.05).  www.nature.com/scientificreports/ Antimicrobial effect of aPDT based on DNA-aptamer-NGO against P. gingivalis in planktonic form. Figure 11 shows the Log 10 CFU/mL reduction rates of P. gingivalis after different treatments as compared to untreated P. gingivalis suspension. According to the findings, 1/2 × and 1/4 × MIC of DNA-aptamer-NGO alone showed a concentration-dependent decrease of 1.49 and 0.73 Log 10 for P. gingivalis, respectively (P < 0.05). Upon irradiation, aPDT with 1/2 × and 1/4 × MIC of DNA-aptamer-NGO led to reductions of 4.33 and 3.42 Log 10 against P. gingivalis, respectively (P < 0.05). In contrast, no significant change in P. gingivalis viability was observed after irradiation of diode laser light (P > 0.05).
Anti-biofilm effect of aPDT based on DNA-aptamer-NGO against P. gingivalis. Since the microbial biofilms are more resistant to antimicrobial treatment, we used an MBC dose of DNA-aptamer-NGO against P. gingivalis in this study. Similar to the effect observed for planktonic cells of P. gingivalis, the results of the crystal violet assay in Fig. 12 show that aPDT using 1/2 × and 1/4 × MBC of DNA-aptamer-NGO plus irradiation  www.nature.com/scientificreports/ of the diode laser light (1 min) has a significantly anti-biofilm effect against P. gingivalis in comparison with the control group (P < 0.05). Although diode laser and 1/4 × MBC of DNA-aptamer-NGO alone were not able to inhibit the biofilm considerably (P > 0.05), a significant biofilm degradation was observed in P. gingivalis biofilm treated with 1/4 × MBC of DNA-aptamer-NGO alone versus the control group (P < 0.05; Fig. 12).

Assessment of anti-metabolic activity of aPDT based on DNA-aptamer-NGO. The aPDT results
showed that the metabolic activity of P. gingivalis was more sensitive to 1/2 × MIC of DNA-aptamer-NGO, which resulted in 40.3% inactivation compared to 1/4 × MBC of DNA-aptamer-NGO, where only 22.2% inactivation was observed after similar light irradiation (both P < 0.05; Fig. 13). In contrast, there was no significant antimetabolic activity was observed in P. gingivalis treated with 1/2 × and 1/4 × MIC of DNA-aptamer-NGO and diode laser alone (all less than 4.0%; P > 0.05).   www.nature.com/scientificreports/ increased in the aPDT groups. According to the results, the percentage of apoptosis cells treated with DNAaptamer-NGO at 1/2 × and 1/4 × MIC plus diode laser were 13.9% and 12.7%, respectively (Fig. 14b).

The apoptotic effects of aPDT based on
Evaluation of genes expression. The expression level of rgpA gene significantly decreased after exposure to aPDT groups compared with the control group (untreated P. gingivalis; P < 0.05; Fig. 15). As shown in Fig. 15, the expression of rgpA gene was downregulated to approximately 6.8-and 4.1-fold following aPDT using 1/2 × and 1/4 × MIC of DNA-aptamer-NGO, respectively (P < 0.05). DNA-aptamer-NGO plus diode laser reduced the expression of fimA gene significantly. The greatest reduction was observed for aPDT using 1/2 × MIC of DNA-aptamer-NGO, which was approximately 10.4-fold (P < 0.05). According to the findings, the profile of oxyR gene expression was enhanced in P. gingivalis cells, with the greatest increase seen for aPDT using 1/2 × and 1/4 × MIC of DNA-aptamer-NGO, which were 4.7-and 3.2-fold, respectively (P < 0.05). On the other hand, there was no significant difference in gene expression when the P. gingivalis were treated with DNA-aptamer-NGO and diode laser alone (P > 0.05).

Discussion
In the current study, targeted identification of P. gingivalis as the most important microorganism involved in periodontitis using DNA-aptamer-NGO was conducted, and the antimicrobial potential of aPDT using DNAaptamer-NGO against P. gingivalis was evaluated. Periodontal diseases ensue following the establishment of polymicrobial subgingival biofilms, and P. gingivalis is the foremost among these microbial pathogens. P. gingivalis can bind to epithelial cells, erythrocytes, fibroblasts, and components of the extracellular matrix via fimbriae and proteolytic enzymes 47 . The systematic use of antibiotics in the treatment of periodontitis is limited due to the need for high doses to achieve the proper concentration of the drug in the gingival sulcus, the rapid onset of bacterial resistance to antibiotics, and the side effects of drugs. In addition, due to the advanced structure and function of the subgingival biofilm, antibiotics may be ineffective or inactivated 48 .
Recently, single antimicrobial agents-carrying drug delivery systems have been introduced to prevent systemic side effects of antibiotics and drug resistance due to oral administration of antibiotics in the treatment of periodontitis 48 . The aptamer can play the role of a specific carrier of antimicrobial agent and increase the effectiveness of treatment, prevent the removal of the beneficial and effective microbiome in health, the development and spread of antibiotic resistance, and the side effects of systemic administration of drugs 49,50 .
Identification of the aptamer candidate is feasible by designing whole-cell SELEX with the addition of a label. Inhere, DNA-aptamer was labeled with FAM and the binding of labeled DNA-aptamer to NGO was carried out based on the modified Lin et al. method 30 . The principle of the detection of P. gingivalis using FAM-modified aptamer is based on the continuous process of quenching the fluorescence of NGO and returning fluorescence in the presence of P. gingivalis. In the absence of P. gingivalis, FAM-aptamer is adsorbed onto the surface of NGO via weak binding force by π-π stacking, and NGO quenches the fluorescence of FAM. In the presence of P. gingivalis, the aptamers fall off from the NGO surface and bind to the P. gingivalis, causing fluorescence restoration.
Tan et al. 51 have shown that the fluorescence quenching of FAM-aptamer occurs rapidly following its binding to the GO surface (i.e. the formation of FAM-aptamer-GO composite) and tends to decrease significantly after 2 min. In contrast, upon the addition of CEM (human acute leukemic lymphoblast cell lines), the CEM-FAM-aptamer was formed slowly and the release of the FAM-aptamer from the GO surface was slower and took more than 30 min. So, the fluorescence quenching by the GO can be gradually restored. Accordingly, during  www.nature.com/scientificreports/ the period when the FAM-aptamer-GO composite is attached to the target and before the GO is released from the target-FAM-aptamer-GO complex, if the light is irradiated on the complex, the effects of aPDT can appear. In this study, DNA aptamers are selected and desorbed from NGO surfaces in the presence of target molecules at close to the neutral pH (pH 7.4 and high ionic strength). A slight increase in the pH (i.e., pH 8.5 and high ionic strength) has been shown to have a positive effect on aptamer binding to the target, and lowering the pH (pH 5.5 and high ionic strength) has had an adverse effect on aptamer binding to the target. The fluorescence intensity of the "aptamer-target complex" at pH 8.5 has been shown to increase slightly in comparison with pH 7.4 while at pH 5.5 no obvious fluorescence intensity has been observed. Huang et al. 32 revealed that the binding equilibrium can be shifted by simply tuning the solution pH. At lower pH (pH 3.5), the aptamer-GO binding is enhanced while the aptamer-target binding is weakened, making this system a regenerable biosensor without covalent conjugation. The acidification of the "target-FAM-aptamer-GO complex" by incubating with 500 mM, pH 3.5, leads to regeneration. At this pH, the FAM-aptamer releases the bound target and re-adsorb onto the GO surface and leading to the formation of the FAM-aptamer-NGO composite. The fact that the pH 3.5 sample showed a much lower fluorescence supported that a low pH was crucial for shuttling the FAM-aptamer back to the GO surface.
On the evaluation of the biosafety aspects of nanomaterials for in vivo, hemocompatibility and cytotoxicity effects should be assessed. In this study, the hemolysis assay was performed to test the hemolytic activity of DNA-aptamer-NGO by studying their effect on erythrocytes. As the results have shown, DNA-aptamer-NGO was compatible with blood cells and the medium remained colorless due to the coagulation property of blood cells. Also, the percentage of cytotoxicity of DNA-aptamer-NGO at different concentrations ranged from 4.8% to 12.4%. No significant difference was observed compared to the control group.
One of the benefits of using an aptamer-based drug delivery system in the treatment of periodontitis is the targeted therapy in the treatment of periodontitis by binding specifically to the organism which aptamer is designed for it. Thus, the microflora effective in creating periodontal health is not destroyed and the possibility of their presence and, as a result, the possibility of returning health to the periodontium is raised. According to the results of this study, DNA-aptamer-NGO demonstrated a preferential binding affinity for P. gingivalis over the other bacteria tested.
Aptamers obtained through the SELEX strategy can bind to target sites. Numerous studies have detailed the selection of aptamers against different microbial species in recent years [52][53][54][55][56][57][58] . Wang et al. 53 , Davydova et al. 54 , and Soundy and Day 55 provided several aptamers as specific bio-recognition molecules for the rapid detection, early diagnosis, and therapeutic targeting of Pseudomonas aeruginosa. The findings of Bayraç et al. 56 suggest that DNAaptamers may be potential probes for further research into the proteins responsible for Streptococcus pneumoniae Figure 15. mRNA expression levels of P. gingivalis following different treatment groups. The relative fold change in mRNA expression levels of P. gingivalis following treatment with 1/2 × and 1/4 × MIC of DNAaptamer-NGO, aPDT (DNA-aptamer-NGO at 1/2 × and 1/4 × MIC plus diode laser), and diode laser were determined using the RT-qPCR. Significant differences according to the control, *P < 0.05. www.nature.com/scientificreports/ biofilm. Hu et al. 57 developed DNA-aptamers for the detection of Bifidobacterium breve. They reported the developed colorimetric bioassay based on the aptamer BB16-11f. is a promising method for the detection of B. breve. In another study, Saad et al. 58 provided a cell-SELEX strategy in identifying two aptamers binding to Legionella pneumophila in a water system with high affinity.

Scientific
To the best of our knowledge, no study has been conducted to investigate the antimicrobial application of DNA-aptamer-NGO during aPDT. In the present study, after confirming the binding of DNA-aptamer-NGO to P. gingivalis, its antimicrobial properties were evaluated in both planktonic and biofilm phases. The pHresponsive DNA-aptamer-NGO-complex could facilitate the accumulation of DNA-aptamer-NGO in bacterial cells and hence greatly improve the effect of aPDT against P. gingivalis. According to the findings, non-toxic and non-hemolytic DNA-aptamer-NGO with diode laser irradiation reduced P. gingivalis Log 10 CFU/mL. Similar to the effect observed for planktonic cells of P. gingivalis, aPDT using DNA-aptamer-NGO had significantly anti-biofilm effect against P. gingivalis. Therefore, not only aptamer specifically identify P. gingivalis as the target bacterium, but it also played an antimicrobial role in the degradation of P. gingivalis biofilm in aPDT process by an NGO-carrying drug delivery system. In addition, the metabolic activity of P. gingivalis was more sensitive to aPDT based on DNA-aptamer-NGO.
The previous studies confirmed the application of aptamers in interference of cell apoptosis [59][60][61][62][63] . It has been proven that aptamers regulate the extrinsic (by activating specific sensors or genes to induce or suppress apoptosis) and intrinsic (by trigging and transducing the apoptotic signals from the extracellular medium to the intracellular medium after targeting death receptors) pathways of apoptotic in the cancer cells 60 . In this study, the apoptotic effect of aPDT using DNA-aptamer-NGO was determined. As the results displayed, although the number of apoptotic cells increased in aPDT groups (1/2 × and 1/4 × MIC plus diode) through ROS generation, these inductions of apoptosis were not significant. Moreover, the anti-virulence activity of DNA-aptamer-NGOmediated aPDT showed that the expression level of genes (rgpA and fimA) involved in bacterial biofilm formation decreased significantly after exposure to 1/2 × and 1/4 × MIC of DNA-aptamer-NGO, while the expression level of oxyR as a gene involved in response to oxidative stress increased considerably; the former reduces the pathogenesis and the latter increases the possibility of elimination of microorganisms.

Conclusion
Based on the results, DNA-aptamer-NGO can detect P. gingivalis in microbial complexes with the highest binding affinity. An increase in the antimicrobial, anti-biofilm, and anti-metabolic, as well as, changes in the expression level of genes involved in pathogenicity followed by the excessive intracellular ROS generation induced by aPDT in the presence of DNA-aptamer-NGO were the main responsible for the significant elimination of P. gingivalis. In conclusion, our results suggest that DNA-aptamer-NGO as a bio-theragnostic element can be used as a promising candidate to detect P. gingivalis in periopathogenic complex in real-time and in situ.